Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.

Different routes for the construction of biologically active diversely functionalized bicyclo[3.3.1]nonanes: an exploration of new perspectives for anticancer chemotherapeutics

Cancer is the second most high-morbidity disease throughout the world. From ancient days, natural products have been known to possess several biological activities, and research on natural products is one of the most enticing areas where scientists are engrossed in the extraction of valuable compounds from various plants to isolate many life-saving medicines, along with their other applications. It has been noticed that the bicyclo[3.3.1]nonane moiety is predominant in most biologically active natural products owing to its exceptional characteristics compared to others. Many derivatives of bicyclo[3.3.1]nonane are attractive to researchers for use in asymmetric catalysis or as potent anticancer entities along with their successful applications as ion receptors, metallocycles, and molecular tweezers. Therefore, this review article discusses several miscellaneous synthetic routes for the construction of bicyclo[3.3.1]nonanes and their heteroanalogues in association with the delineation of their anticancer activities with few selective compounds.

Cyclo[2]carbazole[2]pyrrole: a preorganized calix[4]pyrrole analogue

A cyclo[2]carbazole[2]pyrrole (2) consisting of two carbazoles and two pyrroles has been synthesized by directly linking the carbazole 1- and 8-carbon atoms to the pyrrole α-carbon atoms. Macrocycle 2 is an extensively conjugated 16-membered macrocyclic ring that is fixed in a pseudo-1,3-alternate conformation. This provides a preorganized anion binding site consisting of two pyrrole subunits. ¹H NMR spectroscopic analysis revealed that only the two diagonally opposed pyrrole NH protons, as opposed to the carbazole protons, take part in anion binding. Nevertheless, cyclo[2]carbazole[2]pyrrole 2 binds representative anions with higher affinity in CD₂Cl₂ than calix[4]pyrrole (1), a well-studied non-conjugated tetrapyrrole macrocycle that binds anions via four pyrrolic NH hydrogen bond interactions. On the basis of computational studies, the higher chloride anion affinity of receptor 2 relative to 1 is rationalized in terms of a larger binding energy and a lower host strain energy associated with anion complexation. In the presence of excess fluoride or bicarbonate anions, compound 2 loses two pyrrolic NH protons to produce a stable dianionic macrocycle [2-2H]^2- displaying a quenched fluorescence.

PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking

The physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term "physics-based" is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF. We evaluated the PMFF in three ways. We concluded that the PMFF provides reliable information based on the structure in a biological system and interprets the biological phenomena accurately by providing more accurate evidence of the biological phenomena.

Molecular Dynamics Simulation of Cellulose I-Ethylenediamine Complex Crystal Models

Cellulose I fibrils swell on exposure to ethylenediamine (EDA), which forms the cellulose I-EDA complex. These are regarded as host materials with guest intercalation. The present study reports molecular dynamics (MD) simulations of cellulose I-EDA crystal models with finite fiber to reproduce desorption of EDA molecules. The force field parameters for EDA were improved. Part of the EDA molecules was desorbed only from the surfaces of the crystal models, not from their interiors. The EDA molecules diffused through a hydrophilic channel composed of the hydrophilic edges of the cellulose chains, and their conformations and orientations changed. With the configuration of the cellulose chains being held, the vacant hydrophilic channel was immediately filled with water molecules. The innermost part of the crystal models, defined as a core unit, was partly deformed from the initial crystal structure, including the changes in the exocyclic group conformations of the cellulose chains and the orientations of the EDA molecules, coupled with partial reconfiguration of the intermolecular hydrogen bonding scheme. A possible crystalline conversion scheme after complete desorption of EDA has been discussed based on the present findings.

Reversing Organic-Inorganic Hybrid Perovskite Degradation in Water via pH and Hydrogen Bonds

The moisture instability of organic-inorganic hybrid perovskite solar cells has been a major obstacle to the commercialization, calling for mechanistic understanding of the degradation process, which has been under debate. Here we present a surprising discovery that the degradation is actually reversible, via in situ observation of X-ray diffraction, supported by FTIR and SEM. To isolate the hydrogen bond effect, water was replaced by methanol during the in situ experiment, revealing the decomposition to be initiated by the breakdown of N-H-I hydrogen bonds. This is followed by the step of organic iodide hydrolyzing, which can be inhibited in the neutral environment, making the whole process reversible under variable pH.

Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s

The Platinum dataset of protein-bound ligand conformations was used to benchmark the ability of the MMFF94s force field to generate bioactive conformations by minimization of randomly generated conformers. Torsion angle parameters that generally caused wrong geometries were reparameterized by conducting dihedral scans using ab initio calculations at the MP2 level. This reparameterization resulted in a systematic improvement of generated conformations.

Protein-small molecule docking with receptor flexibility in iMOLSDOCK

We have earlier reported the iMOLSDOCK technique to perform 'induced-fit' peptide-protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLSs) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the optimum pose and conformation. In this paper we report the extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset of 34 protein-ligand complexes as well as with Astex Diverse dataset, with nonpeptide small molecules as ligands. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time. The source code and binary of MOLS 2.0 (under a GNU Lesser General Public License) are freely available for download at https://sourceforge.net/projects/mols2-0/files/ .

Charge transfer dynamics at the boron subphthalocyanine chloride/C60 interface: non-adiabatic dynamics study with Libra-X

The Libra-X software for non-adiabatic molecular dynamics is reported. It is used to comprehensively study the charge transfer dynamics at the boron subphtalocyanine chloride (SubPc)/fullerene (C₆₀) interface.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

A newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit. ParFit is in an open source program available for free on GitHub ( https://github.com/fzahari/ParFit ).

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX-AFITT refinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows. PHENIX-AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein-ligand PDB structures are presented. Refinements using PHENIX-AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. For the data presented, PHENIX-AFITT refinements result in more chemically accurate models for small-molecule ligands.

Bringing the MMFF force field to the RDKit: implementation and validation

A general purpose force field such as MMFF94/MMFF94s, which can properly deal with a wide range of diverse structures, is very valuable in the context of a cheminformatics toolkit. Herein we present an open-source implementation of this force field within the RDKit. The new MMFF functionality can be accessed through a C++/C#/Python/Java application programming interface (API) developed along the lines of the one already available for UFF in the RDKit. Our implementation was fully validated against the official validation suite provided by the MMFF authors. All energies and gradients were correctly computed; moreover, atom type and force constants were correctly assigned for 3D molecules built from SMILES strings. To provide full flexibility, the available API provides direct access to include/exclude individual terms from the MMFF energy expression and to carry out constrained geometry optimizations. The availability of a MMFF-capable molecular mechanics engine coupled with the rest of the RDKit functionality and covered by the BSD license is appealing to researchers operating in both academia and industry.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

Electron momentum spectroscopy of 1-butene: a theoretical analysis using molecular dynamics and molecular quantum similarity

The results of experimental studies of the valence electronic structure of 1-butene by means of electron momentum spectroscopy (EMS) have been reinterpreted on the basis of molecular dynamical simulations in conjunction with the classical MM3 force field. The computed atomic trajectories demonstrate the importance of thermally induced nuclear dynamics in the electronic neutral ground state, in the form of significant deviations from stationary points on the potential energy surface and considerable variations of the C-C-C-C dihedral angle. These motions are found to have a considerable influence on the computed spectral bands and outer-valence electron momentum distributions. Euclidean distances between spherically averaged electron momentum densities confirm that thermally induced nuclear motions need to be fully taken into account for a consistent interpretation of the results of EMS experiments on conformationally flexible molecules.

A predictive science approach to aid understanding of electrospray ionisation tandem mass spectrometric fragmentation pathways of small molecules using density functional calculations

RATIONALE

Tandem mass spectrometry (MS/MS) dissociation pathways can vary markedly between compound classes and can result in challenging and time-consuming interpretation of the data. Compound, class and substructure specific fragmentation rules for protonated molecules require refinement to aid the structural elucidation process.

METHODS

The application of a predictive science approach using density functional theory (DFT) calculations has been investigated to estimate the abundances of first-generation product ions observed using an ion trap mass spectrometer. This has been achieved by application of Boltzmann population theory to electrospray ionisation (ESI)-MS and MS/MS data.

RESULTS

Tandem ESI-MS data for this preliminary study were used to investigate the internal stabilities of protonated species and their product ions. The calculated relative abundances of 11.3%, 96.5%, and 1.1% for the product ion (m/z 192) of three quinazoline structural isomers are compared with the experimental values of 16%, 90% and 0% observed in the first-generation product ion mass spectra.

CONCLUSIONS

Close correlation between calculated and experimental data has been demonstrated for these initial data. Applying this approach and establishing fragmentation rules, based on structure specific and common fragmentation behaviour, would improve and expedite the structural elucidation process.

Photoelectron and electron momentum spectroscopy of tetrahydrofuran from a molecular dynamical perspective

The results of experimental studies of the valence electronic structure of tetrahydrofuran employing He I photoelectron spectroscopy as well as Electron Momentum Spectroscopy (EMS) have been reinterpreted on the basis of Molecular Dynamical simulations employing the classical MM3 force field and large-scale quantum mechanical simulations employing Born-Oppenheimer Molecular Dynamics in conjunction with the dispersion corrected ωB97XD exchange-correlation functional. Analysis of the produced atomic trajectories demonstrates the importance of thermal deviations from the lowest energy path for pseudorotation, in the form of considerable variations of the ring-puckering amplitude. These deviations are found to have a significant influence on several outer-valence electron momentum distributions, as well as on the He I photoelectron spectrum.

Informing mechanistic toxicology with computational molecular models

Computational molecular models of chemicals interacting with biomolecular targets provides toxicologists a valuable, affordable, and sustainable source of in silico molecular level information that augments, enriches, and complements in vitro and in vivo efforts. From a molecular biophysical ansatz, we describe how 3D molecular modeling methods used to numerically evaluate the classical pair-wise potential at the chemical/biological interface can inform mechanism of action and the dose-response paradigm of modern toxicology. With an emphasis on molecular docking, 3D-QSAR and pharmacophore/toxicophore approaches, we demonstrate how these methods can be integrated with chemoinformatic and toxicogenomic efforts into a tiered computational toxicology workflow. We describe generalized protocols in which 3D computational molecular modeling is used to enhance our ability to predict and model the most relevant toxicokinetic, metabolic, and molecular toxicological endpoints, thereby accelerating the computational toxicology-driven basis of modern risk assessment while providing a starting point for rational sustainable molecular design.

Cooperative titanocene and phosphine catalysis: accelerated C-X activation for the generation of reactive organometallics

The study presented herein describes a reductive transmetalation approach toward the generation of Grignard and organozinc reagents mediated by a titanocene catalyst. This method enables the metalation of functionalized substrates without loss of functional group compatibility. Allyl zinc reagents and allyl, vinyl, and alkyl Grignard reagents were generated in situ and used in the addition to carbonyl substrates to provide the corresponding carbinols in yields up to 99%. It was discovered that phosphine ligands effectively accelerate the reductive transmetalation event to enable the metalation of C-X bonds at temperatures as low as -40 °C. Performing the reactions in the presence of chiral diamines and amino alcohols led to the enantioselective allylation of aldehydes.

Searching the "biologically relevant"conformation of dopamine: a computational approach

We report here an exhaustive and complete conformational study on the conformational potential energy hypersurface (PEHS) of dopamine (DA) interacting with the dopamine D2 receptor (D2-DR). A reduced 3D model for the binding pocket of the human D2-DR was constructed on the basis of the theoretical model structure of bacteriorhodopsin. In our reduced model system, only 13 amino acids were included to perform the quantum mechanics calculations. To obtain the different complexes of DA/D2-DR, we combined semiempirical (PM6), DFT (B3LYP/6-31G(d)), and QTAIM calculations. The molecular flexibility of DA interacting with the D2-DR was evaluated from potential energy surfaces and potential energy curves. A comparative study between the molecular flexibility of DA in the gas phase and at D2-DR was carried out. In addition, several molecular dynamics simulations were carried out to evaluate the molecular flexibility of the different complexes obtained. Our results allow us to postulate the complexes of type A as the "biologically relevant conformations" of DA. In addition, the theoretical calculations reported here suggested that a mechanistic stepwise process takes place for DA in which the protonated nitrogen group (in any conformation) acts as the anchoring portion, and this process is followed by a rapid rearrangement of the conformation allowing the interaction of the catecholic OH groups.

Conformational analysis of piperazine and piperidine analogs of GBR 12909: stochastic approach to evaluating the effects of force fields and solvent

Analogs of the flexible dopamine reuptake inhibitor, GBR 12909 (1), may have potential utility in the treatment of cocaine abuse. As a first step in the 3D-QSAR modeling of the dopamine transporter (DAT)/serotonin transporter (SERT) selectivity of these compounds, we carried out conformational analyses of two analogs of 1: a piperazine (2) and a related piperidine (3). Ensembles of conformers consisting of local minima on the potential energy surface of the molecule were generated in the vacuum phase and in implicit solvent by random search conformational analysis using the Tripos and MMFF94 force fields. Some differences were noted in the conformer populations due to differences in the treatment of the tertiary amine nitrogen and ether oxygen atom types by the force fields. The force fields also differed in their descriptions of internal rotation around the C(sp³)-O(sp³) bond proximal to the bisphenyl moiety. Molecular orbital calculations at the HF/6-31G(d) and B3LYP/6-31G(d) levels of C-O internal rotation in model compound (5), designed to model the effect of the proximity of the bisphenyl group on C-O internal rotation, showed a broad region of low energy between -60° to 60° with minima at both -60° and 30° and a low rotational barrier at 0°, in closer agreement with the MMFF94 results than the Tripos results. Molecular mechanics calculations on model compound (6) showed that the MMFF94 force field was much more sensitive than the Tripos force field to the effects of the bisphenyl moiety on C-O internal rotation.

Protein-ligand docking using mutually orthogonal Latin squares (MOLSDOCK)

The theoretical prediction of the association of a flexible ligand with a protein receptor requires efficient sampling of the conformational space of the ligand. Several docking methodologies are currently available. We have proposed a docking technique that performs well at low computational cost. The method uses mutually orthogonal Latin squares to efficiently sample the docking space. A variant of the mean field technique is used to analyze this sample to arrive at the optimum. The method has been previously applied to search through both the conformational space of a peptide as well its docking space. Here we extend this method to simultaneously identify both the low energy conformation as well as a high scoring docking mode for the small organic ligand molecules. Application of the method to 45 protein-ligand complexes, in which the number of rotatable torsions varies from 2 to 19, and comparisons with AutoDock 4.0, showed that the method works well.

Structure and conformational dynamics of trichothecene mycotoxins

A combination of NMR spectroscopy and molecular modeling has been employed to characterize the conformation and dynamics of the macrolide ring in verrucarin A and roridin A, two closely related toxins in the trichothecene mycotoxin family. Longitudinal carbon-13 relaxation times demonstrate the relative flexibility of the macrolide ring. The calculations, NOEs, and scalar vicinal coupling constants show that verrucarin A in CDCl 3 and CD 2Cl 2 predominantly adopts a single, well-defined conformation that matches the crystal structure. In contrast, roridin A is present as a mixture of two conformers.

Syntheses of the Eastern Halves of Ritterazines B, F, G, and H, Leading to Reassignment of the 5,5-Spiroketal Stereochemistry of Ritterazines B and F

The ritterazine class of natural products comprises 26 compounds-all of which are spiroketal-containing steroidal heterodimers-that inhibit the proliferation of cultured human cancer cell lines with IC50 values in the low nanomolar range. Little is known about their chemistry, cellular target(s), or mechanism(s) of growth inhibition, due primarily to the small amount of material available from natural sources. In this paper we report syntheses of the eastern halves of ritterazines B, F, G, and H and address the energetic and mechanistic aspects of spiroketal equilibration for each. These studies have led to reassignment of the 5,5-spiroketal stereochemistry of ritterazines B and F, and they have enabled us to propose a quantitative description of the natural distribution of these ritterazine compounds.

Molecular modeling of hexakis(areneisonitrile)technetium(I), tricarbonyl eta5 cyclopentadienyl technetium and technetium(V)-oxo complexes: MM3 parameter development and prediction of biological properties

Genetic algorithms (GA) were used to develop specific technetium metal-ligand force field parameters for the MM3 force field. These parameters were developed using automated procedures within the program FFGenerAtor from a combination of crystallographic structures and ab initio calculations. These new parameters produced results in good agreement with experiment when tested against a blind validation set. To illustrate the utility of these new force field parameters, quantitative structure-activity relationship (QSAR) models were developed to predict the P-glycoprotein uptake (log10 VI) of a series of hexakis(areneisonitrile)technetium(I) complexes and to predict their biodistribution. The log10 VI QSAR model, built using a training set of 16 Tc(I) isonitrile complexes, exhibited a correlation between the experimental log10 VI and 5 simple descriptors as follows: r2 = 0.94, q2 = 0.93. When applied to an external test set of six Tc(I) isonitrile complexes, the QSAR preformed with great accuracy q2 = 0.78 based on a leave-one-out cross-validation analysis. Further QSAR models were developed to predict the biodistribution of the same set of Tc(I) isonitrile complexes; a QSAR model to predict hepatic uptake exhibited a correlation between the experimental log10(Blood/Liver) with six simple descriptors as follows: r2 = 0.97, q2 = 0.96. A QSAR model to predict renal uptake exhibited a correlation between the experimental log10(Blood/Kidney) and six simple descriptors as follows: r2 = 0.85, q2 = 0.82. When applied to the external test set the QSAR models preformed with great accuracy, q2 = 0.78 and 0.56, respectively.

Divergence en Route to Nonclassical Annonaceous Acetogenins. Synthesis of Pyranicin and Pyragonicin†

Syntheses of the nonclassical annonaceous acetogenins, pyranicin, and pyragonicin from common late-stage intermediates are presented. The construction of key elements relies on asymmetric HWE reactions, including the desymmetrization of a meso-dialdehyde and a parallel kinetic resolution of a racemic aldehyde. A stereoconvergent Pd-catalyzed substitution serves to install the C4 stereocenter in protected form with different orthogonal protective groups. A divergent strategy to form 1,4- and 1,6-diols, employing stereoselective Zn-mediated alkynylations, is used for completion of the core structures. Notably, the stereoselective coupling reaction toward pyragonicin proceeds with highly functionalized fragments. The methodology is further expanded by a divergent synthesis of all stereoisomers of the 2,3,6-trisubstituted tetrahydropyran subunit.

Scaffold hopping with molecular field points: identification of a cholecystokinin-2 (CCK2) receptor pharmacophore and its use in the design of a prototypical series of pyrrole- and imidazole-based CCK2 antagonists

A new molecular modeling approach has been used to derive a pharmacophore of the potent and selective cholecystokinin-2 (CCK(2)) receptor antagonist 5 (JB93182), based on features shared with two related series. The technique uses "field points" as simple and effective descriptions of the electrostatic and van der Waals maxima and minima surrounding a molecule equipped with XED (extended electron distribution) charges. Problems associated with the high levels of biliary elimination of 5 in vivo required us to design a compound with significantly lower molecular weight without sacrificing its nanomolar levels of in vitro activity. Two new series of compounds were designed to mimic the arrangement of field points present in the pharmacophore rather than its structural elements. In a formal sense, two of the three amides in 5 were replaced with either a simple pyrrole or imidazole, while some features thought to be essential for the high levels of in vitro activity of the parent compounds were retained and others deleted. These compounds maintained activity and selectivity for this receptor over CCK(1). In addition, the reduction in molecular weight coupled with lower polarities greatly reduced levels of biliary elimination associated with 5. This makes them good lead compounds for development of drug candidates whose structures are not obviously related to those of the parents and represents the first example of scaffold hopping using molecular field points.

QSAR studies of copper azamacrocycles and thiosemicarbazones: MM3 parameter development and prediction of biological properties

Genetic algorithms (GA) were used to develop specific copper metal-ligand force field parameters for the MM3 force field, from a combination of crystallographic structures and ab initio calculations. These new parameters produced results in good agreement with experiment and previously reported copper metal-ligand parameters for the AMBER force field. The MM3 parameters were then used to develop several quantitative structure-activity relationship (QSAR) models. A successful QSAR for predicting the lipophilicity (log P(ow)) of several classes of Cu(II)-chelating ligands was built using a training set of 32 Cu(II) radiometal complexes and 6 simple molecular descriptors. The QSAR exhibited a correlation between the predicted and experimental log P(ow) with an r(2) = 0.95, q(2) = 0.92. When applied to an external test set of 11 Cu(II) complexes, the QSAR preformed with great accuracy; r(2) = 0.93 and a q(2) = 0.91 utilizing a leave-one-out cross-validation analysis. Additional QSAR models were developed to predict the biodistribution of a smaller set of Cu(II) bis(thiosemicarbazone) complexes.

Validation and use of the MM-PBSA approach for drug discovery

The MM-PBSA approach has become a popular method for calculating binding affinities of biomolecular complexes. Published application examples focus on small test sets and few proteins and, hence, are of limited relevance in assessing the general validity of this method. To further characterize MM-PBSA, we report on a more extensive study involving a large number of ligands and eight different proteins. Our results show that applying the MM-PBSA energy function to a single, relaxed complex structure is an adequate and sometimes more accurate approach than the standard free energy averaging over molecular dynamics snapshots. The use of MM-PBSA on a single structure is shown to be valuable (a) as a postdocking filter in further enriching virtual screening results, (b) as a helpful tool to prioritize de novo design solutions, and (c) for distinguishing between good and weak binders (DeltapIC(50) > or = 2-3), but rarely to reproduce smaller free energy differences.

Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers

The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.